Now I changed the .top file in this way and I am getting this error now :- change :- ; Include forcefield parameters #include "charmm27.ff/forcefield.itp"
;Include ligand topology #include "PTR.itp" [ moleculetype ] ; Name nrexcl Protein_chain_A 3 ===================== error:- Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8# Generated 23220 of the 23220 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 20092 of the 23220 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' ------------------------------------------------------- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype LIG For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- "I Had So Many Problem, and Then I Got Me a Walkman" (F. Black) On Tue, Jun 21, 2011 at 1:56 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 21/06/2011 2:51 PM, bharat gupta wrote: > >> ok now I am doing the things again and here is the result of output of >> each command till adding ions. At the time of executing the command grompp >> for reading em.mdp file for ions.tpr generation, I am getting the following >> error:- >> >> >> Fatal error: >> Syntax error - File PTR.itp, line 7 >> Last line read: >> '[ atomtypes ] ' >> Invalid order for directive atomtypes >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at >> http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors> >> ------------------------------**------------------------- >> >> "Everything's formed from particles" (Van der Graaf Generator) >> >> here's a list of output , I obtained till the step of adding ion ?? >> > > You haven't followed the steps of the tutorial well enough. Specifically, > you've edited a .top or .itp file in the wrong place. > > Mark > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com
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